Investigating the role of centromere variation in non-random aneuploidy and early pregnancy loss

Human reproduction is highly error-prone, resulting in aneuploidy (loss or gain of chromosomes), which is a leading cause of early pregnancy loss (EPL). The mechanisms contributing to chromosomal errors remain poorly understood, precluding development of effective diagnostics or therapeutics for prevention of EPL. This proposal aims to identify genetic variants associated with chromosomal abnormalities in early pregnancy loss cases, crucial for developing intervention strategies to mitigate pre-implantation pregnancy loss. I will investigate this from the perspective of centromeres, an essential chromosomal locus that plays a critical role in accurate chromosome segregation. Emerging evidence suggests that genetic and epigenetic (centromere-associated protein A, CENPA) variation at centromeres may contribute to chromosomal instability. However, the impact of centromere variation on aneuploidy risk in pregnancies remains largely unexplored, highlighting a key area of opportunity for understanding the molecular basis of its development and its role in establishing a healthy pregnancy. My preliminary data suggests that aneuploidy affects chromosomes in a non-random manner, a pattern that is conserved between horses and humans. Additionally, I identified large variation in centromere genetics both between individuals, and across chromosomes within the same individual that could drive non- random aneuploidy. Thus, the overarching objective of this proposal is to investigate how large genetic variation at centromeres impacts aneuploidy rates using a unique, naturally occurring animal model of miscarriage: the horse. The genus Equus provides a unique opportunity to test this hypothesis due to natural variation in centromere organization and access to a well-characterized equine pregnancy loss tissue biobank. Aim 1 will generate a comprehensive atlas of equine centromere genetic variation and, importantly, evaluate which specific variants are associated with aneuploid pregnancy loss cases. Aim 2 will explore the relationship between genetic and epigenetic centromere variation and examine the functional impacts of centromere size asymmetry, arising from large variation in underlying genetics, on aneuploidy risk. I will use 1) cell-based models enhancing centromere genetic mismatches to assess impacts of the resulting size asymmetry on aneuploidy, and (2) early equine embryos with known parental centromere differences to directly evaluate aneuploidy risk in natural conceptions. By identifying centromere-linked risk factors for aneuploidy, this work has the potential to inform new diagnostic tools, including genetic tests that assess aneuploidy risk, with implications for couples experiencing recurrent pregnancy loss and IVF failure. This Fellowship will support my research conducted in a multidisciplinary environment, integrating molecular genetics, bioinformatics, and clinical training in reproductive biology, in alignment with goals of the combined DVM-PhD training plan to bridge basic research and clinical applications in reproductive medicine. Project Number: 1F30HD121356-01 | Fiscal Year: 2026 | NIH Institute/Center: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | Principal Investigator: Anna McKane | Institution: CORNELL UNIVERSITY, ITHACA, NY | Award Amount: $46,594 | Activity Code: F30 | Study Section: Special Emphasis Panel[ZRG1 F06A-D (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11317336